An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions

Varshni Rajagopal, Jeanette Seiler, Isha Nasa, Simona Cantarella, Jana Theiss, Franziska Herget, Bianca Kaifer, Melina Klostermann, Rainer Will, Martin Schneider, Dominic Helm, Julian König, Kathi Zarnack, Sven Diederichs (), Arminja N. Kettenbach () and Maïwen Caudron-Herger ()
Additional contact information
Varshni Rajagopal: German Cancer Research Center (DKFZ)
Jeanette Seiler: German Cancer Research Center (DKFZ)
Isha Nasa: Geisel School of Medicine at Dartmouth
Simona Cantarella: German Cancer Research Center (DKFZ)
Jana Theiss: German Cancer Research Center (DKFZ)
Franziska Herget: German Cancer Research Center (DKFZ)
Bianca Kaifer: German Cancer Research Center (DKFZ)
Melina Klostermann: Buchmann Institute for Molecular Life Sciences
Rainer Will: German Cancer Research Center (DKFZ)
Martin Schneider: German Cancer Research Center (DKFZ)
Dominic Helm: German Cancer Research Center (DKFZ)
Julian König: Institute of Molecular Biology (IMB)
Kathi Zarnack: Buchmann Institute for Molecular Life Sciences
Sven Diederichs: University of Freiburg
Arminja N. Kettenbach: Geisel School of Medicine at Dartmouth
Maïwen Caudron-Herger: German Cancer Research Center (DKFZ)

Nature Communications, 2025, vol. 16, issue 1, 1-24

Abstract: Abstract Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins, which modulate the fate of RNA. Inversely, RNA riboregulates the interactions and functions of the associated proteins. Dysregulation of ribonucleoprotein functions is linked to diseases such as cancer and neurological disorders. In dividing cells, RNA and RNA-binding proteins are present in mitotic structures, but their impact on cell division remains unclear. By applying the proteome-wide R-DeeP strategy to cells synchronized in mitosis versus interphase integrated with the RBP2GO knowledge, we provided an atlas of RNA-dependent proteins in cell division, accessible at R-DeeP3.dkfz.de. We uncovered AURKA, KIFC1 and TPX2 as unconventional RNA-binding proteins. KIFC1 was identified as a new substrate of AURKA, and new TPX2-interacting protein. Their pair-wise interactions were RNA dependent. In addition, RNA stimulated AURKA kinase activity and stabilized its conformation. In this work, we highlighted riboregulation of major mitotic factors as an additional complexity level of cell division.

Date: 2025
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DOI: 10.1038/s41467-025-57671-3

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